Buggy code:
private CyNode createNamedSBaseNode ( NamedSBase sbase , String type ) { } private void copyNodeAttributes ( CyNode sourceNode , CyNode targetNode ) { } private void readCore ( Model model ) { } private void readQual ( Model model , QualModelPlugin qModel ) { SBMLReaderTask . logger . info ( "**<seq2seq4repair_space>qual<seq2seq4repair_space>**" ) ; for ( QualitativeSpecies qSpecies : qModel . getListOfQualitativeSpecies ( ) ) { CyNode node = createNamedSBaseNode ( qSpecies , NODETYPE_QUAL_SPECIES ) ; if ( qSpecies . isSetCompartment ( ) ) { AttributeUtil . set ( network , node , ATTR_COMPARTMENT , qSpecies . getCompartment ( ) , String . class ) ; CyNode comp = nodeById . get ( qSpecies . getCompartment ( ) ) ; CyEdge edge = network . addEdge ( node , comp , true ) ; AttributeUtil . set ( network , edge , INTERACTION_ATTR , INTERACTION_SPECIES_COMPARTMENT , String . class ) ; } if ( qSpecies . isSetConstant ( ) ) { AttributeUtil . set ( network , node , ATTR_CONSTANT , qSpecies . getConstant ( ) , Boolean . class ) ; } if ( qSpecies . isSetInitialLevel ( ) ) { AttributeUtil . set ( network , node , ATTR_QUAL_INITIAL_LEVEL , qSpecies . getInitialLevel ( ) , Integer . class ) ; } if ( qSpecies . isSetMaxLevel ( ) ) { AttributeUtil . set ( network , node , ATTR_QUAL_MAX_LEVEL , qSpecies . getMaxLevel ( ) , Integer . class ) ; } } for ( Transition transition : qModel . getListOfTransitions ( ) ) { CyNode node = createNamedSBaseNode ( transition , NODETYPE_QUAL_TRANSITION ) ; for ( Input input : transition . getListOfInputs ( ) ) { CyNode inNode = nodeById . get ( input . getQualitativeSpecies ( ) ) ; CyEdge edge = network . addEdge ( node , inNode , true ) ; AttributeUtil . set ( network , edge , INTERACTION_ATTR , INTERACTION_QUAL_TRANSITION_INPUT , String . class ) ; AttributeUtil . set ( network , edge , ATTR_QUAL_TRANSITION_EFFECT , input . getTransitionEffect ( ) . toString ( ) , String . class ) ; AttributeUtil . set ( network , edge , ATTR_QUAL_QUALITATIVE_SPECIES , input . getQualitativeSpecies ( ) . toString ( ) , String . class ) ; if ( input . isSetId ( ) ) { AttributeUtil . set ( network , edge , ATTR_ID , input . getId ( ) , String . class ) ; } if ( input . isSetName ( ) ) { AttributeUtil . set ( network , edge , ATTR_NAME , input . getName ( ) , String . class ) ; } if ( input . isSetSign ( ) ) { AttributeUtil . set ( network , edge , ATTR_QUAL_SIGN , input . getSign ( ) . toString ( ) , String . class ) ; } if ( input . isSetSBOTerm ( ) ) { AttributeUtil . set ( network , edge , ATTR_SBOTERM , input . getSBOTermID ( ) , String . class ) ; } if ( input . isSetMetaId ( ) ) { AttributeUtil . set ( network , edge , ATTR_METAID , input . getMetaId ( ) , String . class ) ; } if ( input . isSetThresholdLevel ( ) ) { AttributeUtil . set ( network , edge , ATTR_QUAL_THRESHOLD_LEVEL , input . getThresholdLevel ( ) , Integer . class ) ; } } for ( Output output : transition . getListOfOutputs ( ) ) { CyNode outNode = nodeById . get ( output . getQualitativeSpecies ( ) ) ; CyEdge edge = network . addEdge ( node , outNode , true ) ; AttributeUtil . set ( network , edge , INTERACTION_ATTR , INTERACTION_QUAL_TRANSITION_OUTPUT , String . class ) ; AttributeUtil . set ( network , edge , ATTR_QUAL_QUALITATIVE_SPECIES , output . getQualitativeSpecies ( ) . toString ( ) , String . class ) ; AttributeUtil . set ( network , edge , ATTR_QUAL_TRANSITION_EFFECT , output . getTransitionEffect ( ) . toString ( ) , String . class ) ; if ( output . isSetId ( ) ) { AttributeUtil . set ( network , edge , ATTR_ID , output . getId ( ) , String . class ) ; } if ( output . isSetName ( ) ) { AttributeUtil . set ( network , edge , ATTR_NAME , output . getName ( ) , String . class ) ; } if ( output . isSetSBOTerm ( ) ) { AttributeUtil . set ( network , edge , ATTR_SBOTERM , output . getSBOTermID ( ) , String . class ) ; } if ( output . isSetMetaId ( ) ) { AttributeUtil . set ( network , edge , ATTR_METAID , output . getMetaId ( ) , String . class ) ; } if ( output . isSetOutputLevel ( ) ) { AttributeUtil . set ( network , edge , ATTR_QUAL_OUTPUT_LEVEL , output . getOutputLevel ( ) , String . class ) ; } } if ( transition . isSetListOfFunctionTerms ( ) ) { List < Integer > resultLevels = new LinkedList < Integer > ( ) ; for ( FunctionTerm term : transition . getListOfFunctionTerms ( ) ) { resultLevels . add ( term . getResultLevel ( ) ) ; } <START_BUG> AttributeUtil . set ( network , node , ATTR_QUAL_RESULT_LEVELS , resultLevels , List . class ) ; <END_BUG> } } } private void readFBC ( Model model , FBCModelPlugin fbcModel ) { } private void processAssociation ( CyNode parentNode , String parentType , Association association ) { } private void readLayouts ( Model model , QualModelPlugin qualModel , LayoutModelPlugin layoutModel ) { } private void readLayout ( Model model , QualModelPlugin qualModel , Layout layout ) { } @ Override public CyNetwork [ ] getNetworks ( ) { } @ Override public CyNetworkView buildCyNetworkView ( final CyNetwork network ) { } private static String readString ( InputStream source ) throws IOException { } public void cancel ( ) { } }

Fix:
AttributeUtil . setList ( network , node , ATTR_QUAL_RESULT_LEVELS , resultLevels , Integer . class ) ;